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The abundance of intestinal flora is closely related to human diseases, but diseases are not caused by a single gut microbe. Instead, they result from the complex interplay of numerous microbial entities. This intricate and implicit…
Microbiome `omics approaches can reveal intriguing relationships between the human microbiome and certain disease states. Along with the identification of specific bacteria taxa associated with diseases, recent scientific advancements…
The Lotka-Volterra model is widely used to model interactions between two species. Here, we generate synthetic data mimicking competitive, mutualistic and antagonistic interactions between two tumor cell lines, and then use the…
Microbiome functions are encoded within the genes of the community-wide metagenome. A natural question is whether properties of a microbial community can be predicted just from knowing the raw DNA sequences of its members. In this work, we…
A model of population genetics of the Lotka-Volterra type with mutations on a statistical manifold is introduced. Mutations in the model are described by diffusion on a statistical manifold with a generator in the form of a Laplace-Beltrami…
Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large…
The skin microbiome plays an important role in the maintenance of a healthy skin. It is an ecosystem, composed of several species, competing for resources and interacting with the skin cells. Imbalance in the cutaneous microbiome, also…
Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for…
This paper serves as a framework for designing advanced models for drug action on metabolism. Drug treatment may affect metabolism by either enhancing or inhibiting metabolic reactions comprising a metabolic network. We introduce the…
Empirical observations show that ecological communities can have a huge number of coexisting species, also with few or limited number of resources. These ecosystems are characterized by multiple type of interactions, in particular…
Empirical observations show that ecological communities can have a huge number of coexisting species, also with few or limited number of resources. These ecosystems are characterized by multiple type of interactions, in particular…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
The human body consists of microbiomes associated with the development and prevention of several diseases. These microbial organisms form several complex interactions that are informative to the scientific community for explaining disease…
The tremendous boost in the next generation sequencing and in the omics technologies makes it possible to characterize human gut microbiome (the collective genomes of the microbial community that reside in our gastrointestinal tract). While…
Real ecosystems are characterized by sparse and asymmetric interactions, posing a major challenge to theoretical analysis. We introduce a new method to study the generalized Lotka-Volterra model with stochastic dynamics on sparse graphs. By…
Plants rarely occur in isolated systems. Bacteria can inhabit either the endosphere, the region inside the plant root, or the rhizosphere, the soil region just outside the plant root. Our goal is to understand if using genomic data and…
During the last decades macroecology has identified broad-scale patterns of abundances and diversity of microbial communities and put forward some potential explanations for them. However, these advances are not paralleled by a full…
As antibiotic resistance continues to pose a significant threat to public health, alternative treatments are urgently needed. Phage therapy, which utilizes bacteriophages to specifically target bacterial pathogens, has emerged as a…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…
Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial…